2Y5M

STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 7.7 MONOACYLGLYCEROL LIPID CUBIC PHASE.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AL4PDB ENTRY 1AL4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.525 %(W/V) PEG 3350, 0.2 M LISO4, 0.1 M BIS TRIS AT PH 5.5, LIPIDIC CUBIC PHASE OF 7.7 MAG (SN-1-O-(CIS-7)TETRADECENYLGLYCEROL) WAS USED IN A RATIO OF 1:20 (MOL/MOL) GRAMICIDIN D TO LIPID.
Crystal Properties
Matthews coefficientSolvent content
2.5852.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.639α = 90
b = 62.794β = 100.02
c = 30.664γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MX-300SI(111) DOUBLE CRYSTAL2008-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.0830.294.90.115.86.34643525.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.081.1650.422.43.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1AL41.0830.244055238094.950.131670.130410.15461RANDOM12.7
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.340.11-0.650.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.474
r_sphericity_free16.436
r_dihedral_angle_3_deg9.794
r_sphericity_bonded7.531
r_scangle_it7.117
r_scbond_it5.307
r_dihedral_angle_1_deg4.732
r_mcangle_it4.018
r_rigid_bond_restr2.878
r_mcbond_it2.828
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.474
r_sphericity_free16.436
r_dihedral_angle_3_deg9.794
r_sphericity_bonded7.531
r_scangle_it7.117
r_scbond_it5.307
r_dihedral_angle_1_deg4.732
r_mcangle_it4.018
r_rigid_bond_restr2.878
r_mcbond_it2.828
r_angle_refined_deg1.704
r_mcbond_other1.368
r_angle_other_deg0.813
r_chiral_restr0.151
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_bond_other_d0.007
r_gen_planes_other0.002
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms816
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing